Anti-codon

But perhaps the discovery that caused the greatest surprise was the presence of these substituted adenine derivatives in the anti-codon loops of several transfer RNAs—not only in plant tRNAs but in those for serine and tyrosine in yeast (Bergquist and Matthews, 1962) in E. coli and probably in all other organisms. 

The m-RNA strand is thus arranged in a series of units, each three bases long, each of which represents, or codes for, a particular amino acid. Corresponding to these three m-RNA bases are a complementary set of three bases on the arm of the t-RNA molecule directly opposite the arm which binds the amino acid, and these three nucleotides form base-pairs with the m-RNA triplet on the ribosome. Bach triplet of three bases along the m-RNA is termed a codon the complementary triplet on the t-RNA is called an anti-codon. 

Let us look more cl osely at the molecular events at the ribosome, where the recognition and formation of peptide bonds actually occurs. We have seen that the ribosome is composed of two different subunits, but only one of these subunits, the smaller of the two, is essential for initiation of protein synthesis, although it must be associated with the larger unit before chain elongation can proceed. Initiation also requires the presence of an energy source (supplied not by ATP but GTP), a particular amino acyl t-RNA whose anti-codon corresponds to the start here codon on m-RNA and, at least in bacteria, three soluble protein initiation factors called IF1, IF2, IF3. The ribosome has two sites for t-RNA binding, the P site and the A site, but only initiator t-RNA can bind to the P site - all other incoming amino acyl t-RNAs bind to the A site. 

The principle of the Wobble Hypothesis, showing the various codon/anti codon base pairings that are possible when the first position in the tRNA anticodon (50 to 30) is a U, G, or I. 

Transfer RNA (tRNA) plays the role of carrying an amino acid to the synthesis site at the ribosome. tRNA molecules are relatively small, with around seventy-five nucleotides in a single strand. They form several loops, one of which is an anti-codon, a three-residue series that is complementary to the codon present in the mRNA (Figure 2). The opposite end of the tRNA is where an amino acid is bound. The correct binding of an amino acid to a specific tRNA is every bit as important as the anti-codon in ensuring that the correct amino acid is incorporated in the polypeptide that is synthesized. There are different tRNA molecules for each of the twenty amino acids that are present in living systems some amino acids have more than one tRNA that carry them to the synthesis site. 

Elongation ultimately requires the repetition of several steps (1) The tRNA-amino acid complexes must be made. (2) This complex must bind to the mRNA-ribosome assembly site. The correct amino acid is assured by the matching of the anti-codon on the tRNA to the codon on the mRNA. 

Figure 1.81 Two depictions of transfer RNA (tRNA) (pdb ltn2). (a) Surface Display in which the Van der Waals surface of all atoms is shown and negative charge (red areas). This display clearly demonstrates the bent shape of the molecule (b) Rings Display in which phosphodiester backbone is shown as an arrowed ribbon (green/black) ribose rings (green), purine bases (red) and pyrimidine (blue) bases are shown in structural outline (c) Rings Display of distorted A-form RNA helix that forms part of the acceptor stem of tRNA. Both anti-codon loop and 3 -acceptor stem are illustrated given their functional importance in translation (see Section 1.4.6).

This is a lysyl tRNA synthetase enzyme in the first instance that should have the expected capacity to couple the naturally available amino acid L-lysine to appropriate cognate tRNAs bearing anti-codon sequences complementary to lysine codons (see Section 1.6.1). However in the presence of zinc ions, Zn +, the function of this enzyme becomes altered to catalyse the biosynthesis of diadenosine-5, (Ap4A) followed by... 

Once associated with mRNA, the pre-initiation complex scans downstream to locate a start codon (AUG). This process is driven by ATP, and requires the helicase activity of an elF. The start codon is recognised by base paring between the anti-codon on tRNA and the AUG on the mRNA. Codon-anticodon interaction is facilitated by yet more elFs. Usually, the first AUG codon that is encountered is used, especially if it is surrounded by the so called Kozak consensus sequence (named after its discoverer Marilyn Kozak). Occasionally a later AUG is used if the first AUG not in the context of a consensus Kozak sequence, or is very close to the 5 cap. This is in contrast to prokaryotes, where the AUG that will act as a start codon is located at the future P site by the position of the ribosome after base-pairing between the 16S rRNA of the ribosome and the Shine Dalgamo sequence. 

The selection of aa-tRNA at the A site of the ribosome is determined by the specific interaction between the codon of mRNA and the anti-codon of tRNA. A... 

As a general principle, translation is the step in which the nucleotide sequence of messenger RNA is translated into a definite amino-acid sequence, using the adaptor transfer RNAs decoding units. As stated before, the recognition mechanism between messenger RNA and transfer RNAs is of the codon-anti-codon type. 

As mentioned earlier, RNA synthesis is catalyzed by the RNA polymerase in all organisms. Prokaryotes express a single RNA polymerase used for synthesis of all RNAs, while eukaryotes encode multiple RNA polymerases with dedicated functions. RNA polymerase I (Pol I) in eukaryotic cells is responsible for synthesis of ribosomal RNA, which accounts for more than 70% of total RNA in the cell. Pol III catalyzes synthesis of small RNA molecules, including transfer RNAs which bring in appropriate amino acids to the ribosome for protein synthesis by using their anti-codon triplet bases. Pol II is responsible for synthesis of all other RNA, specifically mRNA. 

To avoid competition between endogenous release factor and suppressor tRNA, a new strategy based on frameshift suppression mutations was developed. " " This strategy, based on the ability of tRNAs with extended anti-codons to suppress frameshift mutations, has two advantages over conventional suppression using the three-base amber, opal, and ochre stop codons competition between tRNA and release factors (RF) is avoided, and this approach allows more than one unnatural amino acid to be incorporated... 

Taki, M., Hohsaka, T, Murakami, H., Taira, K., and Sisido, M., Position-specific incorporation of a fluorophore-quencher pair into a single streptavidin through orthogonal four-base codon/anti-codon pairs,/. Am. Chem. Soc., 124,49,14586, 2002. 

Fig. 9.9. Simplified possible structure of a t-RNA (serine specific) showing the nucleotide chain where the amino acid is attached, the anti-codon triplet and the position of the IPA...

---